An Olive Ridley sea turtle (Lepidochelys olivacea) make its way to the sea after being released at San Diego beach in La Libertad, 34 kms south of San Salvador, on August 17, 2013

"Some say it could be due to climate change, sea currents or the techniques used by fishermen," said biologist Ivan Ramirez of the Foundation for the Sustainable Development of Nicaragua (Fundenic).

The head of wildlife and ecosystems at the Salvadoran environment ministry, Nestor Herrera, said the strongest hypothesis over the death of the turtles is that they were killed by saxitoxin—which affects the nervous system and can be produced by a red tide.

In one area of El Salvador's coast, dogs that started eating dead turtles stopped breathing and died almost instantly.

In 2006, saxitoxin killed about 500 sea turtles in El Salvador, and four years later, another 100 died of the same cause.

However, there is a red tide almost every year, while such widespread turtle deaths have never happened before, said Angel Ibarra, coordinator of Ecological Unity of El Salvador, who added more study is needed to shed light on the phenomenon.

Others worry that the recent spate of turtle deaths can be traced more directly to human activity.

In Guatemala, the National Council of Protected Areas said some turtles are caught up by industrial-size fishing boats that drag nets along the sea bed and capture everything in their path, a process called trawling.

And drift net fishing, in which very long nets float behind a ship and near the surface of the water, could also be a threat to turtles.

Jose Leonidas Gomez, who works with a sea turtle conservation project in El Salvador, said turtles discovered dead on one beach were found not to have eaten, so it is presumed they got caught in nets.

Biologist Fabio Buitrago of Nicaragua's Fundenic said turtles are also being killed by fishermen who use explosives, among other techniques.

"The fishermen themselves say so," he said.

Antonio Benavides, a veteran turtle conservationist in El Salvador, said protecting the creatures is all the more difficult because the mortality rate for juveniles is already high.

Only one out of a thousand babies that hatch and make it out into the sea ever returns to the beach as an adult to lay eggs.

Fertility is yet another issue: in September scientists in Honduras said turtles on one beach laid 40 percent fewer eggs.